Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes

Planctopirus limnophila belongs to the bacterial phylum Planctomycetes, a relatively understudied lineage with remarkable cell biology features. Here, we report a genome-wide analysis of essential gene content in P. limnophila. We show that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most other studied bacteria, are not essential for growth under laboratory conditions in this species. We identify essential genes likely involved in lipopolysaccharide biosynthesis, consistent with the view of Planctomycetes as diderm bacteria, and highlight other essential genes of unknown functions. Furthermore, we explore potential stages of evolution of the essential gene repertoire in Planctomycetes and the related phyla Verrucomicrobia and Chlamydiae. Our results provide insights into the divergent molecular and cellular biology of Planctomycetes.

This PDF file includes: a) Supplementary Tables S1 to S4. b) Supplementary Figures S1 to S5. Supplementary Table 1.LPS and outer membrane genes.

Gene name COG Locus tag Essentiality
. Complete phyletic distribution of P. limnophila essential genes.NOG heatmap according to the EggNOG database annotations for the P. limnophila essential gene set.Each row represents the essential genes reported in this work with a NOG.The KEGG ID of the gene encoding the protein is located to the right of each row, followed by the NOG with its functional category and function.Each column represents one of the 50 selected classes.The color inside the heatmap reflects the degree of distribution of a particular NOG in each class, with red representing complete distribution in all selected organisms of that class and light yellow representing absence in all selected organisms of that class.Source data are provided as a Source Data file. .Complete phyletic distribution of E. coli essential genes.NOG heatmap according to the EggNOG database annotations for the E. coli essential gene set.Each row represents the essential genes reported by Goodall et al. with a NOG.The GenBank ID of the gene encoding the protein is located to the right of each row, followed by the NOG with its functional category and function.Each column represents one of the 50 selected classes.The color inside the heatmap reflects the degree of distribution of a particular NOG in each class, with red representing complete distribution in all selected organisms of that class and light yellow representing absence in all selected organisms of that class.Source data are provided as a Source Data file.
FigureS4.Complete phyletic distribution of E. coli essential genes.NOG heatmap according to the EggNOG database annotations for the E. coli essential gene set.Each row represents the essential genes reported by Goodall et al. with a NOG.The GenBank ID of the gene encoding the protein is located to the right of each row, followed by the NOG with its functional category and function.Each column represents one of the 50 selected classes.The color inside the heatmap reflects the degree of distribution of a particular NOG in each class, with red representing complete distribution in all selected organisms of that class and light yellow representing absence in all selected organisms of that class.Source data are provided as a Source Data file.

Figure S5 .
Figure S5.Deletion mutant checking PCR.a) PCR using primers annealing upstream and downstream to the flanking regions used as homologous sequences to obtain the deletion mutants.Expected sizes are indicated in bp in panel b.Primers used are shown in Sup.Table 4. L = DNA molecular weight ladder (Kbp) M = Mutant; Wt = Wild type; P = Plasmid; -= Negative control (H 2 O).* Amplicon was sequenced to verify the PCR due to the similar size expected.
Insertion index distribution in P. limnophila.The red curve represents the fit of the left part of this distribution to an exponential distribution.The blue curve represents the fit of the right-hand side to a gamma distribution.The green and orange lines represent the cut-offs used for the fits of the distributions.The histogram and curves represent probability densities, with the histogram normalized such that the total area under the bars is 1. Figure S2.Visualization of "domain essential" proteins.The vertical lines represents the transposon insertion sites in each of the represented proteins.Pfam protein domains are represented in different colors with their corresponding Pfam ID.The X-axis represents the protein length in amino acids.a) Proteins reported as unclear.b) Proteins reported as nonessential.